MolNFT v1 · #126069 · protein
Structure of CEZANNE/OTUD7B otu domain bound to LYS11-linked diubiquitin
5LRV · Otu domain-containing protein 7B: “Structure of CEZANNE/OTUD7B otu domain bound to LYS11-linked diubiquitin”. X-ray diffraction, 2 ligands (ABU, PO4), 2 pockets (best druggability 0.70). MolNFT v1 #126069 on GenesisL1: 3D structure…
- PDB
- 5LRV
- Type
- protein
- Length
- 432 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Otu domain-containing protein 7B; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q6GQQ9, P0CG47
- Ligands
- ABU, PO4
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Otu domain-containing protein 7B (EC 3.4.19.12) | protein | 286 | 40% helix, 15% strand | Q6GQQ9 |
| B | Polyubiquitin-B | protein | 71 | 27% helix, 31% strand | P0CG47 |
| C | Polyubiquitin-B | protein | 75 | 20% helix, 33% strand | P0CG47 |
Ligands and binding sites
- ABU · Gamma-amino-butanoic acid · ligand · chains A, B, C
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.70 | 0.81 | 59 | empty |
| 2 | 231 | 0.52 | 0.76 | 42 | GOL |
Interfaces
2 interfaces between chains.
- A–C · 1035 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 800 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 5LRV · Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GQQ9 · AlphaFold monomer V2.0 prediction for otu domain-containing protein 7B (Q6GQQ9) · a predicted model of the same protein · chain A against A, TM-score 0.88
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6GQQ9
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5LRV · PDBe 5LRV · UniProt Q6GQQ9 · UniProt P0CG47
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